De novo design of transmembrane helix–helix interactions and measurement of stability in a biological membrane

Membrane proteins regulate a large number of cellular functions, and have great potential as tools for manipulation of biological systems. Developing these tools requires a robust and quantitative understanding of membrane protein folding and interactions within the bilayer. With this in mind, we have designed a series of proteins to probe the net thermodynamic contribution of well-known sequence motifs to transmembrane helix-helix association in a biological membrane. The proteins were designed from first principles (de novo) using current knowledge about membrane insertion and stabilizing interaction motifs. A simple poly-Leu “scaffold” was decorated with individual helix interaction motifs (G-XXX-G, polar residues, heptad repeat) to create transmembrane helix–helix interactions of increasing strength. The GALLEX assay, an in vivo assay for measurement of transmembrane helix self-association, was combined with computational methods to characterize the relative strength and mode of interaction for each sequence. In addition, the apparent free energy contribution (ΔΔG^app) of each motif to transmembrane helix self-association was measured in a biological membrane, results that are the first of their kind for these de novo designed sequences, and suggest that the free energy barrier to overcoming weak association is quite small (< 1.4 kcal mol^− 1) in a natural membrane. By quantifying and rationalizing the contribution of key motifs to transmembrane helix association, our work offers a route to direct the design of novel sequences for use in biotechnology or synthetic biology (e.g. molecular switches) and to predict the effects of sequence modification in known transmembrane domains (for control of cellular processes).     

Complete mitochondrial genome of Coelomactra antiquata (Mollusca: Bivalvia): The first representative from the family Mactridae with novel gene order and unusual tandem repeats

The complete mitochondrial genome plays an important role in the accurate inference of phylogenetic relationships among metazoans. Mactridae, also known as trough shells or duck clams, is an important family of marine bivalve clams in the order Veneroida. Here we present the complete mitochondrial genome sequence of the Xishishe Coelomactra antiquata (Mollusca: Bivalvia), which is the first representative from the family Mactridae. The mitochondrial genome of C. antiquata is of 17,384 bp in length, and encodes 35 genes, including 12 protein-coding, 21 transfer RNA, and 2 ribosomal RNA genes. Compared with the typical gene content of animal mitochondrial genomes, atp8 and tRNAS₂ are missing. Gene order of the mitochondrial genome of C. antiquata is unique compared with others from Veneroida. In the mitochondrial genome of the C. antiquata, a total of 2189 bp of non-coding nucleotides are scattered among 26 non-coding regions. The largest non-coding region contains one section of tandem repeats (99 bp × 11), which is the second largest tandem repeats found in the mitochondrial genomes from Veneroida. The phylogenetic trees based on mitochondrial genomes support the monophyly of Veneridae and Lucinidae, and the relationship at the family level: ((Veneridae + Mactridae) + (Cardiidae + Solecurtidae)) + Lucinidae. The phylogenetic result is consistent with the morphological classification. Meanwhile, bootstrap values are very high (BP = 94–100), suggesting that the evolutionary relationship based on mitochondrial genomes is very reliable.     

Hereditary spastic paraplegia-like disorder due to a mitochondrial ATP6 gene point mutation

Hereditary spastic paraplegia refers to a genetically heterogeneous syndrome. We identified five members of a family suffering from a late-onset spastic paraplegia-like disorder, carrying the homoplasmic m.9176 T > C mutation in the mitochondrial ATP6 gene. The clinical severity of the disease observed in the family was correlated with the biochemical and assembly defects of the ATP synthase. The m.9176 T > C mutation has been previously associated to Leigh syndrome or familial bilateral striatal necrosis. Other factors such as modifying genes may be involved in the phenotypic expression of the disease. The family belongs to the mitochondrial haplogroup J, previously shown to play a role in modulating the phenotype of mitochondrial diseases and be associated with longevity. Moreover other nuclear modifying genes or environmental factors may contribute to the disease phenotype. This finding extends the genetic heterogeneity of the hereditary spastic paraplegia together with the clinical spectrum of mutations of the ATP6 gene.     

The determinants of hydrophobic mismatch response for transmembrane helices

Hydrophobic mismatch arises from a difference in the hydrophobic thickness of a lipid membrane and a transmembrane protein segment, and is thought to play an important role in the folding, stability and function of membrane proteins. We have investigated the possible adaptations that lipid bilayers and transmembrane α-helices undergo in response to mismatch, using fully-atomistic molecular dynamics simulations totaling 1.4 μs. We have created 25 different tryptophan-alanine-leucine transmembrane α-helical peptide systems, each composed of a hydrophobic alanine–leucine stretch, flanked by 1–4 tryptophan side chains, as well as the β-helical peptide dimer, gramicidin A. Membrane responses to mismatch include changes in local bilayer thickness and lipid order, varying systematically with peptide length. Adding more flanking tryptophan side chains led to an increase in bilayer thinning for negatively mismatched peptides, though it was also associated with a spreading of the bilayer interface. Peptide tilting, bending and stretching were systematic, with tilting dominating the responses, with values of up to ~ 45° for the most positively mismatched peptides. Peptide responses were modulated by the number of tryptophan side chains due to their anchoring roles and distributions around the helices. Potential of mean force calculations for local membrane thickness changes, helix tilting, bending and stretching revealed that membrane deformation is the least energetically costly of all mismatch responses, except for positively mismatched peptides where helix tilting also contributes substantially. This comparison of energetic driving forces of mismatch responses allows for deeper insight into protein stability and conformational changes in lipid membranes.     

Cooperative dynamics of a DNA polymerase replicating complex

Engineered DNA polymerases continue to be the workhorses of many applications in biotechnology, medicine and nanotechnology. However, the dynamic interplay between the enzyme and the DNA remains unclear. In this study, we performed an extensive replica exchange with flexible tempering (REFT) molecular dynamics simulation of the ternary replicating complex of the archaeal family B DNA polymerase from the thermophile Thermococcus gorgonarius, right before the chemical step. The convoluted dynamics of the enzyme are reducible to rigid-body motions of six subdomains. Upon binding to the enzyme, the DNA double helix conformation changes from a twisted state to a partially untwisted state. The twisted state displays strong bending motion, whereby the DNA oscillates between a straight and a bent conformation. The dynamics of double-stranded DNA are strongly correlated with rotations of the thumb toward the palm, which suggests an assisting role of the enzyme during DNA translocation. In the complex, the primer–template duplex displays increased preference for the B-DNA conformation at the n ? 2 and n ? 3 dinucleotide steps. Interactions at the primer 3′ end indicate that Thr541 and Asp540 are the acceptors of the first proton transfer in the chemical step, whereas in the translocation step both residues hold the primer 3′ terminus in the vicinity of the priming site, which is crucial for high processivity.     

Influence of the g− conformation of Ser and Thr on the structure of transmembrane helices

In order to study the influence of Ser and Thr on the structure of transmembrane helices we have analyzed a database of helix stretches extracted from crystal structures of membrane proteins and an ensemble of model helices generated by molecular dynamics simulations. Both complementary analyses show that Ser and Thr in the g? conformation induce and/or stabilize a structural distortion in the helix backbone. Using quantum mechanical calculations, we have attributed this effect to the electrostatic repulsion between the side chain Oγ atom of Ser and Thr and the backbone carbonyl oxygen at position i ? 3. In order to minimize the repulsive force between these negatively charged oxygens, there is a modest increase of the helix bend angle as well as a local opening of the helix turn preceding Ser/Thr. This small distortion can be amplified through the helix, resulting in a significant displacement of the residues located at the other side of the helix. The crystal structures of aquaporin Z and the β₂-adrenergic receptor are used to illustrate these effects. Ser/Thr-induced structural distortions can be implicated in processes as diverse as ligand recognition, protein function and protein folding.     

A novel three-TMH Na+/H+ antiporter and the functional role of its oligomerization

Na⁺/H⁺ antiporters are a category of ubiquitous transmembrane proteins with various important physiological roles in almost all living organisms ranging from bacteria to humans. However, the knowledge of novel Na⁺/H⁺ antiporters remains to be broadened, and the functional roles of oligomerization in these antiporters have not yet been thoroughly understood. Here, we reported functional analysis of an unknown transmembrane protein composed of 103 amino acid residues. This protein was found to function as a Na⁺(Li⁺, K⁺)/H⁺ antiporter. To the best of our knowledge, this antiporter is the minimal one of known Na⁺/H⁺ antiporters and thus designated as NhaM to represent the minimal Na⁺/H⁺ antiporter. NhaM and its homologs have not yet been classified into any protein family. Based on phylogenetic analysis and protein alignment, we propose NhaM and its homologs to constitute a novel transporter family designated as NhaM family. More importantly, we found that NhaM is assembled with parallel protomers into a homo-oligomer and oligomerization is vital for the function of this antiporter. This implies that NhaM may adopt and require an oligomer structure for its normal function to create a similar X-shaped structure to that of the NhaA fold. Taken together, current findings not only present the proposal of a novel transporter family but also positively contribute to the functional roles of oligomerization in Na⁺/H⁺ antiporters.     

Quantifying ‘normal’ shoulder muscle activity during abduction

The purpose of this experiment was to obtain electromyographic (EMG) activity from a sample of healthy shoulders to allow a reference database to be developed and used for comparison with pathological shoulders. Temporal and intensity shoulder muscle activation characteristics during a coronal plane abduction/adduction movement were evaluated in the dominant healthy shoulder of 24 subjects. Surface and intramuscular fine wire electrodes recorded EMG activity from 15 shoulder muscles (deltoid × 3, trapezius × 3, subscapularis × 2, latissimus dorsi, pectoralis major, pectoralis minor, supraspinatus, infraspinatus, serratus anterior and rhomboids) at 2000 Hz for 10 s whilst each subject performed 10 dynamic coronal plane abduction/adduction movements from 0° to 166° to 0° with a light dumbbell. Results revealed that supraspinatus (?.102 s before movement onset) initiated the movement with middle trapezius (?.019 s) and middle deltoid (?.014 s) also activated before the movement onset. Similar patterns were also found in the time of peak amplitude and %MVC with a pattern emerging where the prime movers (supraspinatus and middle deltoid) were among the first to reach peak amplitude or display the highest %MVC values. In conclusion, the most reproducible patterns of activation arose from the more prime mover muscle sites in all EMG variables analysed and although variability was present, there emerged ‘invariant characteristics’ that were considered ‘normal’ for this group of non pathological shoulders. The authors believe that the methodology and certain parts of the analysis in this study can be duplicated and used by future researchers who require a reference database of muscle activity for use as a control group in comparisons to their respective pathological shoulder group.     

The spermatozoon of Mengenilla moldrzyki (Strepsiptera,Mengenillidae): Ultrastructure and phylogenetic considerations

Even though the spermatozoa of several strepsipteran species were described earlier, no data were available for the basal family Mengenillidae. Well-fixed material of the recently described Tunisian species Mengenilla moldrzyki was used for a detailed examination of the sperm ultrastructure. The total length is c. 30 μm. The head region contains a conical acrosome vesicle (0.3-0.35 μm) and an elongated nucleus (7.3 μm) with dense chromatin. Some granular material along with a uniformely dense centriole adjunct and two mitochondrial derivatives are visible at the posterior end of the nucleus. The material of the centriole adjunct does not extend along the flagellum and accessory bodies are absent. The mitochondrial derivatives are elongated structures crossed by a longitudinal crista but lacking parallel transverse cristae and paracrystalline material in the dense matrix. The mitochondrial derivatives gradually reduce their size and end at the most posterior tail region. The flagellar axoneme has a 9 + 9 + 2 pattern and originates beneath the nucleus. In the terminal tail region the axoneme gradually disintegrates. Despite the extreme specialization of the endoparasitc group, strepsipteran spermatozoa are mostly characterized by plesiomorphies. The pattern within the order is largely uniform, but Mengenilla displays several apomorphic features compared to the presumptive strepsipteran groundplan (e.g., absence of crystallizations and cristae in the mitochondrial derivatives). The subdivision of the intertubular material into two compartments with a dense beak-like structure adhering to the tubular wall supports a clade Coleopterida (=Strepsiptera + Coleoptera) + Neuropterida.     

Arabidopsis KEA2, a homolog of bacterial KefC,encodes a K+/H+ antiporter with a chloroplast transit peptide

KEA genes encode putative K⁺ efflux antiporters that are predominantly found in algae and plants but are rare in metazoa; however, nothing is known about their functions in eukaryotic cells. Plant KEA proteins show homology to bacterial K⁺ efflux (Kef) transporters, though two members in the Arabidopsis thaliana family, AtKEA1 and AtKEA2, have acquired an extra hydrophilic domain of over 500 residues at the amino terminus. We show that AtKEA2 is highly expressed in leaves, stems and flowers, but not in roots, and that an N-terminal peptide of the protein is targeted to chloroplasts in Arabidopsis cotyledons. The full-length AtKEA2 protein was inactive when expressed in yeast; however, a truncated AtKEA2 protein (AtsKEA2) lacking the N-terminal domain complemented disruption of the Na⁺(K⁺)/H⁺ antiporter Nhx1p to confer hygromycin resistance and tolerance to Na⁺ or K⁺ stress. To test transport activity, purified truncated AtKEA2 was reconstituted in proteoliposomes containing the fluorescent probe pyranine. Monovalent cations reduced an imposed pH gradient (acid inside) indicating AtsKEA2 mediated cation/H⁺ exchange with preference for K⁺ = Cs⁺ > Li⁺ > Na⁺. When a conserved Asp⁷²¹ in transmembrane helix 6 that aligns to the cation binding Asp¹⁶⁴ of Escherichia coli NhaA was replaced with Ala, AtsKEA2 was completely inactivated. Mutation of a Glu⁸³⁵ between transmembrane helix 8 and 9 in AtsKEA2 also resulted in loss of activity suggesting this region has a regulatory role. Thus, AtKEA2 represents the founding member of a novel group of eukaryote K⁺/H⁺ antiporters that modulate monovalent cation and pH homeostasis in plant chloroplasts or plastids.     

Increased proton leak and SOD2 expression in myotubes from obese non-diabetic subjects with a family history of type 2 diabetes

Muscle insulin resistance is linked to oxidative stress and decreased mitochondrial function. However, the exact cause of muscle insulin resistance is still unknown. Since offspring of patients with type 2 diabetes mellitus (T2DM) are susceptible to developing insulin resistance, they are ideal for studying the early development of insulin resistance. By using primary muscle cells derived from obese non-diabetic subjects with (FH +) or without (FH ?) a family history of T2DM, we aimed to better understand the link between mitochondrial function, oxidative stress, and muscle insulin resistance. Insulin-stimulated glucose uptake and glycogen synthesis were normal in FH + myotubes. Resting oxygen consumption rate was not different between groups. However, proton leak was higher in FH + myotubes. This was associated with lower ATP content and decreased mitochondrial membrane potential in FH + myotubes. Surprisingly, mtDNA content was higher in FH + myotubes. Oxidative stress level was not different between FH + and FH ? groups. Reactive oxygen species content was lower in FH + myotubes when differentiated in high glucose/insulin (25 mM/150 pM), which could be due to higher oxidative stress defenses (SOD2 expression and uncoupled respiration). The increased antioxidant defenses and mtDNA content in FH + myotubes suggest the existence of compensatory mechanisms, which may provisionally prevent the development of insulin resistance.     

The inheritance of pathogenic mitochondrial DNA mutations

Mitochondrial DNA mutations cause disease in > 1 in 5000 of the population, and ～ 1 in 200 of the population are asymptomatic carriers of a pathogenic mtDNA mutation. Many patients with these pathogenic mtDNA mutations present with a progressive, disabling neurological syndrome that leads to major disability and premature death. There is currently no effective treatment for mitochondrial disorders, placing great emphasis on preventing the transmission of these diseases. An empiric approach can be used to guide genetic counseling for common mtDNA mutations, but many families transmit rare or unique molecular defects. There is therefore a pressing need to develop techniques to prevent transmission based on a solid understanding of the biological mechanisms. Several recent studies have cast new light on the genetics and cell biology of mtDNA inheritance, but these studies have also raised new controversies. Here we compare and contrast these findings and discuss their relevance for the transmission of human mtDNA diseases.     

Multiple Symmetrical Lipomatosis — A mitochondrial disorder of brown fat

Multiple Symmetrical Lipomatosis (MSL) is an unusual disorder characterized by the development of axial lipomas in adulthood. The pathoetiology of lipoma tissue in MSL remains unresolved. Seven patients with MSL were followed for a mean period of 12 years (8–20 years). All patients had cervical lipomas ranging from subtle lesions to disfiguring masses; six patients had peripheral neuropathy and five had proximal myopathy. Myoclonus, cerebellar ataxia and additional lipomas were variably present. All patients showed clinical progression. Muscle histopathology was consistent with mitochondrial disease. Five patients were positive for mtDNA point mutation m.8344A > G, three of whom underwent lipoma resection — all samples were positive for uncoupling protein-1 mRNA (unique to brown fat). Lipoma from one case stained positive for adipocyte fatty-acid protein-2 (unique to brown fat and immature adipocytes). This long-term study hallmarks the phenotypic heterogeneity of MSL's associated clinical features. The clinical, genetic and molecular findings substantiate the hypothesis that lipomas in MSL are due to a mitochondrial disorder of brown fat.     

Human mitochondrial haplogroup H: The highest VO2max consumer – Is it a paradox?

Mitochondrial background has been demonstrated to influence maximal oxygen uptake (VO_2max, in mL kg^?1 min^?1), but this genetic influence can be compensated for by regular exercise. A positive correlation among electron transport chain (ETC) coupling, ATP and reactive oxygen species (ROS) production has been established, and mitochondrial variants have been reported to show differences in their ETC performance. In this study, we examined in detail the VO_2max differences found among mitochondrial haplogroups. We recruited 81 healthy male Spanish Caucasian individuals and determined their mitochondrial haplogroup. Their VO_2max was determined using incremental cycling exercise (ICE). VO_2max was lower in J than in non-J haplogroup individuals (P = 0.04). The H haplogroup was responsible for this difference (VO_2max; J vs. H; P = 0.008) and this group also had significantly higher mitochondrial oxidative damage (mtOD) than the J haplogroup (P = 0.04). In agreement with these results, VO_2max and mtOD were positively correlated (P = 0.01). Given that ROS production is the major contributor to mtOD and consumes four times more oxygen per electron than the ETC, our results strongly suggest that ROS production is responsible for the higher VO_2max found in the H variant. These findings not only contribute to a better understanding of the mechanisms underneath VO_2max, but also help to explain some reported associations between mitochondrial haplogroups and mtOD with longevity, sperm motility, premature aging and susceptibility to different pathologies.     

Different effects of novel mtDNA G3242A and G3244A base changes adjacent to a common A3243G mutation in patients with mitochondrial disorders

Two novel mitochondrial DNA base changes were identified at both sides of the 3243A > G mutation, the most common mutation associated with mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS). One was a 3244G > A transition in a girl with MELAS. The other was a 3242G > A transition in a girl with a mitochondrial disorder without a MELAS phenotype. Although the two base changes were adjacent to the 3243A > G mutation, they had different effects on the clinical phenotype, muscle pathology, and respiratory chain enzyme activity. Investigations of the different effects of the 3244G > A and 3242G > A base changes may provide a better understanding of tRNA dysfunction in mitochondrial disorders.     

Variability in the substitution rates between mitochondrial cytochrome c oxidase subunit II domains

We investigated the variability in amino acid sequences between mitochondrial cytochrome c oxidase subunit II (COII) domains, as well as that of gene sequences encoding the corresponding domains. According to the secondary structure, COII consisted of five domains of N- and C-terminal regions posited in the intermembrane space, two transmembrane helices (TM1 and TM2) in the lipid bilayer, and a matrix-embedded loop (ML) that intervened between the two helices. Our analysis, using dictyopteran insects as model species, revealed that amino acid and nucleotide substitution rates were heterogeneous between the COII domains. The amino acid substitution rates were higher in the TM1 (0.380 ± 0.123) and ML domains (0.416 ± 0.184), whereas they were relatively lower in the N-terminal (0.204 ± 0.123) and TM2 domains (0.184 ± 0.088). As expected by the variability in the amino acid substitution rates, the average nucleotide substitution rates were also relatively higher in the TM1 (0.312 ± 0.081) and ML domains (0.302 ± 0.093), whereas the lowest substitution rate was observed in the N domain (0.191 ± 0.073). These results indicate that the heterogeneous substitution rates between COII domains, as well as genes encoding the domains, might be closely related to the inner membrane environment where each region of the amino acid sequence is laid.     

A maze-lover's dream: Burrow architecture,natural history and habitat characteristics of Ansell's mole-rat (Fukomys anselli)

The Ansell's mole-rat (Fukomys anselli, Bathyergidae) is a small-sized social subterranean rodent whose distribution is confined to the Lusaka area in Zambia. It is an established model species for various laboratory studies, but until now the knowledge of its biology under natural conditions has been limited. Here, we provide the first comprehensive natural history and ecological data on a free living population from Miombo woodland. The Ansell's mole-rat lives in groups of up to 13 individuals (mean 9.7 ± 2.5; N = 9 complete, fully established family groups) with a single breeding pair per group. The family groups occupy very large and complex burrow systems consisting of 0.5–2.8 km of tunnels (mean = 1.2 ± 0.6 km, N = 15), which are densely branched and reticulated especially around nests. Burrow systems of neighbouring family groups were often interconnected by a freely passable tunnel, which has never before been documented in any African mole-rats. Mole-rat food density in the study area was relatively low (10.0 ± 8.4 m^?2) but its biomass was large (457 ± 889 g m^?2). This, together with a relatively workable soil (cone resistance = 529 ± 26 N cm^?2 at the end of June, with 10% soil humidity), indicates moderate ecological conditions, which disagrees with the aridity food-distribution hypothesis (AFDH) considering small body size and sociality in bathyergids adaptations to harsh environments.     

Mitochondrial calcium uniporter blocker effectively prevents brain mitochondrial dysfunction caused by iron overload

AimsAlthough iron overload induces oxidative stress and brain mitochondrial dysfunction, and is associated with neurodegenerative diseases, brain mitochondrial iron uptake has not been investigated. We determined the role of mitochondrial calcium uniporter (MCU) in brain mitochondria as a major route for iron entry. We hypothesized that iron overload causes brain mitochondrial dysfunction, and that the MCU blocker prevents iron entry into mitochondria, thus attenuating mitochondrial dysfunction.Main methodsIsolated brain mitochondria from male Wistar rats were used. Iron (Fe^2 + and Fe^3 +) at 0–286 μM were applied onto mitochondria at various incubation times (5–30 min), and the mitochondrial function was determined. Effects of MCU blocker (Ru-360) and iron chelator were studied.Key findingsBoth Fe^2 + and Fe^3 + entered brain mitochondria and caused mitochondrial swelling in a dose- and time-dependent manner, and caused mitochondrial depolarization and increased ROS production. However, Fe^2 + caused more severe mitochondrial dysfunction than Fe^3 +. Although all drugs attenuated mitochondrial dysfunction caused by iron overload, only an MCU blocker could completely prevent ROS production and mitochondrial depolarization.SignificanceOur findings indicated that iron overload caused brain mitochondrial dysfunction, and that an MCU blocker effectively prevented this impairment, suggesting that MCU could be the major portal for brain mitochondrial iron uptake.